Previously defined variants of uncertain significance may play an important role in epilepsy and interactions between certain variants may become pathogenic

This is the authors' abstract. We don't add key points for this paper.

Objective Epilepsy is a chronic neurological disorder related to various etiologies and the prevalence of active epilepsy is estimated to be between 4-10 per 1000 individuals having a significant role of genetic mutations. Next-Generation Sequencing (NGS) panels are utilized for genetic testing, still, a substantial proportion of the results remain uncertain and are not considered directly causative of epilepsy. This study aimed to reevaluate pediatric patients diagnosed with epilepsy who underwent genetic investigation using NGS panels, focusing on inconclusive variant findings or multiple Variants of Uncertain Significance (VUSs). Methods A subgroup of pediatric patients aged 0-25 years, diagnosed with epilepsy, who underwent genetic investigation with an NGS epilepsy panel at the Child Neurology Unit, The Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, between 2018-2022 through Invitae, was reevaluated. Patients with inconclusive variant findings or multiple VUSs in their test results were included. Genetic data were analyzed, focusing on identifying potentially pathogenic variants and frequent genetic combinations. Results Two unrelated potentially pathogenic variants were identified in the SCN9A and QARS1 genes. A frequent genetic combination, RANBP2&RYR3, was also observed among other combinations. The RANBP2 gene consistently co-occurred with RYR3 variants in uncertain results, suggesting potential pathogenicity. Analysis of unaffected parents’ data revealed certain combinations inherited from different parents, suggesting specific gene combinations as potential risk factors for the disease. Significance This study highlights the importance of reevaluating genetic data from pediatric epilepsy patients with inconclusive variant findings or multiple VUSs. Identification of potentially pathogenic variants and frequent genetic combinations, such as RANBP2&RYR3, could aid in understanding the genetic basis of epilepsy and identifying potential hotspots. Plain Language Summary We have performed a retrospective analysis on a subpopulation of pediatric patients diagnosed with epilepsy, we have found that specific genetic variants were repeatable indicating their potential pathogenicity to the disease. Key points 60% of pediatric patients undergoing genetic testing receive an uncertain result emphasizing the complexity of genetic interpretation in epilepsy diagnostics. Pathogenic variants in genes like SCN1A were common, underlining the importance of targeted gene sequencing. Variants in genes like SCN9A and QARS1, currently classified as VUSs, showed consistent presence in epilepsy patients, indicating potential pathogenicity. Specific genetic combinations, such as RANBP2&RYR3, were frequently observed among uncertain results, suggesting potential pathogenicity.